References
- Vlassov AV, Magdaleno S, Setterquist R, et al. Exosomes: current knowledge of their composition, biological functions, and diagnostic and therapeutic potentials. Biochim Biophys Acta Gen Subj. 2012;1820(7):940–12.
- Yáñez-Mó M, Siljander PR-M, Andreu Z, et al. Biological properties of extracellular vesicles and their physiological functions. J Extracell Vesicles. 2015;4(1):27066.
- van der Pol E, Böing AN, Harrison P, et al. Classification, functions, and clinical relevance of extracellular vesicles. Pharmacol Rev. 2012;64(3):676–705.
- Catalanotto C, Cogoni C, Zardo G. MicroRNA in control of gene expression: an overview of nuclear functions. Int J Mol Sci. 2016;17(10):1712.
- Zhang D, Lee H, Zhu Z, et al. Enrichment of selective miRNAs in exosomes and delivery of exosomal miRNAs in vitro and in vivo. Am J Physiol Lung Cell Mol Physiol. 2017;312(1):L110–l121.
- Colombo M, Raposo G, Théry C. Biogenesis, secretion, and intercellular interactions of exosomes and other extracellular vesicles. Annu Rev Cell Dev Biol. 2014;30(1):255–289.
- Kowal J, Tkach M, Théry C. Biogenesis and secretion of exosomes. Curr Opin Cell Biol. 2014;29:116–125.
- Janas T, Janas MM, Sapoń K, et al. Mechanisms of RNA loading into exosomes. FEBS Lett. 2015;589(13):1391–1398.
- Gould SJ, Raposo G. As we wait: coping with an imperfect nomenclature for extracellular vesicles. J Extracell Vesicles. 2013;2(1).
- Turpin D, Truchetet M-E, Faustin B, et al. Role of extracellular vesicles in autoimmune diseases. Autoimmun Rev. 2016;15(2):174–183.
- Srinivasan S, Su M, Ravishankar S, et al. TLR-exosomes exhibit distinct kinetics and effector function. Sci Rep. 2017;7:41623.
- Enderle D, Spiel A, Coticchia CM, et al. Characterization of RNA from exosomes and other extracellular vesicles isolated by a novel spin column-based method. Plos One. 2015;10(8):e0136133.
- Baran-Gale J, Kurtz CL, Erdos MR, et al. Addressing bias in small RNA library preparation for sequencing: a new protocol recovers microRNAs that evade capture by current methods. Front Genet. 2015;6:352.
- Hafner M, Renwick N, Brown M, et al. RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA. 2011;17(9):1697–1712.
- Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical bayes methods. Biostatistics. 2007;8(1):118–127.
- Campbell JD, Liu G, Luo L, et al. Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data. Rna. 2015;21(2):164–171.
- Git A, Dvinge H, Salmon-Divon M, et al. Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA. 2010;16(5):991–1006.
- Blondal T, Brunetto MR, Cavallone D, et al. Genome-wide comparison of next-generation sequencing and qPCR platforms for microRNA profiling in serum. Methods Mol Biol. 2017;1580:21–44.
- Hon KW, Abu N, Ab Mutalib N-S, et al. Exosomes as potential biomarkers and targeted therapy in colorectal cancer: a mini-review. Front Pharmacol. 2017;8:583.
- Mitchell PJ, Welton J, Staffurth J, et al. Can urinary exosomes act as treatment response markers in prostate cancer? J Transl Med. 2009;7(1):4.
- McIntyre LM, Lopiano KK, Morse AM, et al. RNA-seq: technical variability and sampling. BMC Genomics. 2011;12:293.
- Jayaprakash AD, Jabado O, Brown BD, et al. Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing. Nucleic Acids Res. 2011;39(21):e141-e141. e141-e141.
- Consortium, S.M.-I., et al.A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the sequencing quality control consortium. Nat Biotechnol. 2014;32(9):903–914.
- Giraldez MD, Spengler RM, Etheridge A, et al. Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling. Nat Biotechnol. 2018;36(8):746–757.
- Hendricks GMAG,G. Protocol 191: analysis of rAAv sample morphology using negative staining and high resolution electron microscopy. In: Sambrook MRGAJ, editor. Molecular cloning (A laboratory manual). Long Island, New York: Cold Spring Harbor Press; 2012. p. 1301–1303.
- Suárez H, Gámez-Valero A, Reyes R, et al. A bead-assisted flow cytometry method for the semi-quantitative analysis of Extracellular Vesicles. Sci Rep. 2017;7(1):11271.
- Srinivasan S, Vannberg FO, Dixon JB. Lymphatic transport of exosomes as a rapid route of information dissemination to the lymph node. Sci Rep. 2016;6:24436.
- Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods. 2001;25(4):402–408.
- Andrews S, FastQC: a quality control tool for high throughput sequence data. Available from: http://www.bioinformatics.babraham.ac.uk/projects/fastqc, 2010.
- Ewels P, Magnusson M, Lundin S, et al. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32(19):3047–3048.
- Seco-Cervera M, González-Rodríguez D, Ibáñez-Cabellos JS, et al. Small RNA-seq analysis of circulating miRNAs to identify phenotypic variability in Friedreich’s ataxia patients. Sci Data. 2018;5:180021.
- Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal. 2011;17(1):10–12.
- Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357.
- consortium TR. RNAcentral: a comprehensive database of non-coding RNA sequences. Nucleic Acids Res. 2017;45(D1):D128–d134.
- Dillies M-A, Rau A, Aubert J, et al. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief Bioinform. 2013;14(6):671–683.